Pathways [a.k.a GRanMPa (Graph-based Ranking of Mutated Pathways)]

Pathways computes importance scores for a a list of metabolic pathways.

Pathways is an adaptation of Verbeke et al.'s approach that ranks pathways by integrating multiple types of data (gene expression, mutation, methylation and copy number data) together with a gene interaction network. Pathways is focused on uniquely using mutation data to rank the importance of a set of genes (i.e pathways) for a group of samples(i.e genomes).

• Free software: MIT license
• Documentation: https://pathways.readthedocs.io.

Features

• TODO

Installation

It's recommended to install pathways into a virtual environment:

1. Clone the public repository:

   $ git clone https://git.scicore.unibas.ch/TBRU/pathways.git

   or:

   $ git clone ssh://git@git.scicore.unibas.ch:2222/TBRU/pathways.git

2. Assuming you have Anaconda2 installed, with Conda, create a new environment with the Intel distribution for Python 3.6:

   $ conda config --add channels intel
   $ conda create -n pathways -c intel python=3.6 icu=58 scipy numpy pandas matplotlib

   PS: The conda environment should be stored at $HOME/.conda/envs

3. Activate the environment and install python-igraph package from conda-forge:

   $ source activate pathways
   $ conda install -c conda-forge python-igraph pycairo

4. Install pathways:

   $ cd pathways
   $ python setup.py install

   or:

   $ pip install

Documentation

For now (requires flake8):

$ make docs

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.